added smart distance feature and optimized all commands using line by line processing

[mothur.git] / heatmapcommand.cpp

diff --git a/heatmapcommand.cpp b/heatmapcommand.cpp
index 09dfb5a15bde8e52a967c1ef9cdae0e4130a0b3a..c9f6ae524fe7121d59b6538f061830ad522182cd 100644 (file)
--- a/heatmapcommand.cpp
+++ b/heatmapcommand.cpp
@@ -40,6 +40,8 @@ HeatMapCommand::~HeatMapCommand(){
 int HeatMapCommand::execute(){
        try {
                int count = 1;  
+               RAbundVector* lastRAbund;
+               vector<SharedRAbundVector*> lastLookup;
        
                if (format == "sharedfile") {
                        //you have groups
@@ -48,50 +50,126 @@ int HeatMapCommand::execute(){
                        
                        input = globaldata->ginput;
                        lookup = input->getSharedRAbundVectors();
+                       lastLookup = lookup;
                }else if (format == "list") {
                        //you are using just a list file and have only one group
                        read = new ReadOTUFile(globaldata->inputFileName);      
                        read->read(&*globaldata); 
                        
                        rabund = globaldata->rabund;
+                       lastRAbund = globaldata->rabund;
                        input = globaldata->ginput;             
                }
                
+               //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
+               set<string> processedLabels;
+               set<string> userLabels = globaldata->labels;
+
                if (format != "list") { 
                
-                       while(lookup[0] != NULL){
+                       //as long as you are not at the end of the file or done wih the lines you want
+                       while((lookup[0] != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
                
                                if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){                   
        
                                        cout << lookup[0]->getLabel() << '\t' << count << endl;
                                        heatmap->getPic(lookup);
+                                       
+                                       processedLabels.insert(lookup[0]->getLabel());
+                                       userLabels.erase(lookup[0]->getLabel());
                                }
                                
-                               //prevent memory leak
-                               for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
+                               if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
+                                       cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+                                       heatmap->getPic(lastLookup);
+                                       
+                                       processedLabels.insert(lastLookup[0]->getLabel());
+                                       userLabels.erase(lastLookup[0]->getLabel());
+                               }
                                
+                               //prevent memory leak
+                               if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
+                               lastLookup = lookup;                    
+
                                //get next line to process
                                lookup = input->getSharedRAbundVectors();                               
                                count++;
                        }
                        
+                       //output error messages about any remaining user labels
+                       set<string>::iterator it;
+                       bool needToRun = false;
+                       for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+                               cout << "Your file does not include the label "<< *it; 
+                               if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
+                                       cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+                                       needToRun = true;
+                               }else {
+                                       cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+                               }
+                       }
+               
+                       //run last line if you need to
+                       if (needToRun == true)  {
+                               cout << lastLookup[0]->getLabel() << '\t' << count << endl;
+                               heatmap->getPic(lastLookup);
+                       }
+               
+                       for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
+                       
                        //reset groups parameter
                        globaldata->Groups.clear();  
                        
                }else{
                
-                       while(rabund != NULL){
-               
+                       while((rabund != NULL) && ((globaldata->allLines == 1) || (userLabels.size() != 0))) {
+
                                if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(rabund->getLabel()) == 1){                      
        
                                        cout << rabund->getLabel() << '\t' << count << endl;
                                        heatmap->getPic(rabund);
+                                       
+                                       processedLabels.insert(rabund->getLabel());
+                                       userLabels.erase(rabund->getLabel());
                                }
                                
-                               delete rabund;
+                               if ((anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastRAbund->getLabel()) != 1)) {
+
+                                       cout << lastRAbund->getLabel() << '\t' << count << endl;
+                                       heatmap->getPic(lastRAbund);
+                                       
+                                       processedLabels.insert(lastRAbund->getLabel());
+                                       userLabels.erase(lastRAbund->getLabel());
+                               }               
+                               
+                               if (count != 1) { delete lastRAbund; }
+                               lastRAbund = rabund;                    
+
                                rabund = input->getRAbundVector();
                                count++;
                        }
+                       
+                       //output error messages about any remaining user labels
+                       set<string>::iterator it;
+                       bool needToRun = false;
+                       for (it = userLabels.begin(); it != userLabels.end(); it++) {  
+                               cout << "Your file does not include the label "<< *it; 
+                               if (processedLabels.count(lastRAbund->getLabel()) != 1) {
+                                       cout << ". I will use " << lastRAbund->getLabel() << "." << endl;
+                                       needToRun = true;
+                               }else {
+                                       cout << ". Please refer to " << lastRAbund->getLabel() << "." << endl;
+                               }
+                       }
+               
+                       //run last line if you need to
+                       if (needToRun == true)  {
+                               cout << lastRAbund->getLabel() << '\t' << count << endl;
+                               heatmap->getPic(lastRAbund);
+                       }
+               
+                       delete lastRAbund;
+
                }
                
                globaldata->setGroups("");